I have found two bad remastering mistakes so far, and as luck would have it, they are in sister episodes. They are mostly editorial errors, and they are both images depicted on a viewing screen. I'm looking at Blu-Ray Season 2, Doomsday Machine and Immunity Syndrome.

mistake 1

Doomsday: Kirk is on the Constellation and is getting his view screen working. Washburn says "Try it now, Captain." Kirk says "Yes I think...What the devil's going on?"

The error occurs here. In the original version, the cut to the view screen immediately shows the Enterprise firing at the Doomsday cone. That is what Kirk is reacting to.

In the remastered version, the view screen shows static interference on the screen FIRST, then it fades to the Enterprise and the cone. In the remastered cut, Kirk would not have any reason to say "What the devil's going on?" because he hasn't seen the Enterprise yet. Furthermore, the remastered version shows the screen with only the Enterprise in it, firing phasers, which weakens the logic of Kirk's reaction still further! Then later the cone comes into the screen view. Opinions on this? I think it hurts the scene a lot.

mistake 2

In Immunity, just prior to the appearance of the hole in space, Kirk says "scanners on". In the original version, it cuts to the view screen -- stars only. Then later, as you recall, Spock says "I would assume....that." At this point, the hole in space is first shown.

The error in the remastered version? Kirk says "scanners on" and the hole in space already appears on the screen, a full 18 seconds before it is supposed to appear.

I would welcome the submission of any other known remastering errors (but not aesthetic "mistakes" in the effects -- unless you feel you must.) Paramount, can you please repair my disks? David? Mike? Lucille? Anyone? ;o)